A B C D E F G H I L M N P R S T U V W X

R

random - Static variable in class procope.tools.Tools

Globally used random number generator, uses a Mersenne twister

randomizeByExchanging() - Method in class procope.data.complexes.ComplexSet

Returns a randomized copy of the complex set.

randomizeByRemapping() - Method in class procope.data.complexes.ComplexSet

Returns a randomized copy of the complex set.

randomizeByRewiring() - Method in class procope.data.networks.ProteinNetwork

Randomizes a network by rewiring.

randomizeByRewiring(int) - Method in class procope.data.networks.ProteinNetwork

Randomizes a network by rewiring.

rankArray(Comparable<?>[]) - Static method in class procope.tools.math.SpearmanCoefficient

Calculates the ranking for a given array of comparable objects.

readAnnotations(String) - Static method in class procope.evaluation.complexquality.go.GOAnnotationReader

Reads annotations from a given annotations file.

readAnnotations(String, int) - Static method in class procope.evaluation.complexquality.go.GOAnnotationReader

Reads annotations from a given annotations file.

readAnnotations(File) - Static method in class procope.evaluation.complexquality.go.GOAnnotationReader

Reads annotations from a given annotations file.

readAnnotations(File, int) - Static method in class procope.evaluation.complexquality.go.GOAnnotationReader

Reads annotations from a given annotations file.

readAnnotations(InputStream) - Static method in class procope.evaluation.complexquality.go.GOAnnotationReader

Reads annotations from a given input stream.

readAnnotations(InputStream, int) - Static method in class procope.evaluation.complexquality.go.GOAnnotationReader

Reads annotations from a given input stream.

readComplexes(String) - Static method in class procope.data.complexes.ComplexSetReader

Reads complexes from a given file.

readComplexes(String, String) - Static method in class procope.data.complexes.ComplexSetReader

Reads complexes from a given file.

readComplexes(File) - Static method in class procope.data.complexes.ComplexSetReader

Reads complexes from a given file.

readComplexes(File, String) - Static method in class procope.data.complexes.ComplexSetReader

Reads complexes from a given file.

readComplexes(InputStream) - Static method in class procope.data.complexes.ComplexSetReader

Reads complexes from a given InputStream.

readComplexes(InputStream, String) - Static method in class procope.data.complexes.ComplexSetReader

Reads complexes from a given InputStream.

readLocalizationData(String) - Static method in class procope.data.LocalizationDataReader

Reads localization data from a given file.

readLocalizationData(File) - Static method in class procope.data.LocalizationDataReader

Reads localization data from a given file.

readLocalizationData(InputStream) - Static method in class procope.data.LocalizationDataReader

Reads localization data from an input stream

readNetwork(String) - Static method in class procope.data.networks.NetworkReader

Reads an undirected network from a given file.

readNetwork(String, boolean) - Static method in class procope.data.networks.NetworkReader

Reads a network from a given file.

readNetwork(File) - Static method in class procope.data.networks.NetworkReader

Reads an undirected network from a given file.

readNetwork(File, boolean) - Static method in class procope.data.networks.NetworkReader

Reads a network from a given file.

readNetwork(InputStream) - Static method in class procope.data.networks.NetworkReader

Reads an undirected network from a given InputStream.

readNetwork(InputStream, boolean) - Static method in class procope.data.networks.NetworkReader

Reads a network from a given InputStream.

readPurifications(String) - Static method in class procope.data.purifications.PurificationDataReader

Read purification data from a given file.

readPurifications(String, boolean) - Static method in class procope.data.purifications.PurificationDataReader

Read purification data from a given file.

readPurifications(File) - Static method in class procope.data.purifications.PurificationDataReader

Read purification data from a given file.

readPurifications(File, boolean) - Static method in class procope.data.purifications.PurificationDataReader

Read purification data from a given file.

readPurifications(InputStream) - Static method in class procope.data.purifications.PurificationDataReader

Read purification data from a given input stream.

readPurifications(InputStream, boolean) - Static method in class procope.data.purifications.PurificationDataReader

Read purification data from a given input stream.

removeComplex(int) - Method in class procope.data.complexes.ComplexSet

Removes the complex at the specified index from the complex set.

removeComplex(Complex) - Method in class procope.data.complexes.ComplexSet

Removes a given complex from the complex set.

removeComplexesByScore(ProteinNetwork, float) - Method in class procope.data.complexes.ComplexSet

Removes all complexes from the complex set whose average edge score between all proteins of the complex regarding a given scores network is below the cutoff.

removeComplexesByScore(ProteinNetwork, float, boolean) - Method in class procope.data.complexes.ComplexSet

Removes all complexes from the complex set whose average edge score between all proteins of the complex regarding a given scores network is below the cutoff.

removeComplexesBySize(int, boolean) - Method in class procope.data.complexes.ComplexSet

Removes all complexes smaller or larger than a given threshold from the complex set.

removeProtein(Integer) - Method in class procope.data.complexes.Complex

Removes a given protein from the complex.

removeProteinIndex(int) - Method in class procope.data.complexes.Complex

Removes the protein at a given index from the complex.

removeSingletons() - Method in class procope.data.complexes.ComplexSet

Removes singletons from the complex set.

reportNode(int) - Method in interface procope.data.networks.NetworkSearchCallback

Implemented by network search callback adapters.

resolveSynonym(String) - Method in class procope.tools.namemapping.Synonyms

Returns the identifier a synonym is mapped to or id directly of no synonym is associated with that string.

restrictToProteins(Set<Integer>, boolean) - Method in class procope.data.complexes.ComplexSet

Returns a new complex set containing only those complexes whose proteins are completely or partially contained in a given set of proteins.

restrictToProteins(ProteinSet, boolean) - Method in class procope.data.networks.ProteinNetwork

Returns a new network object which contains only those edges where one or both adjacent proteins are contained in a given set of proteins.

restrictToProteins(Set<Integer>, boolean) - Method in class procope.data.networks.ProteinNetwork

Returns a new network object which contains only those edges where one or both adjacent proteins are contained in a given set of proteins.

restrictToProteinSpace(ProteinSet, boolean) - Method in class procope.data.complexes.ComplexSet

Returns a new complex set containing only those complexes whose proteins are completely or partially contained in a given set of proteins.

ROC - Class in procope.evaluation.networkperformance

Contains static methods to calculate ROC curves for protein networks.

ROCCurve - Class in procope.evaluation.networkperformance

An immutable list of ROC points, result of a ROC curve calculation

ROCCurve(List<ROCPoint>) - Constructor for class procope.evaluation.networkperformance.ROCCurve

Constructor which initializes the ROC curve with a given list of points

ROCCurveHandler - Class in procope.evaluation.networkperformance

Contains static functions for writing ROC curves to files and creating actual plots from the ROC curves using Gnuplot or the JFreeChart library.

ROCCurveHandler() - Constructor for class procope.evaluation.networkperformance.ROCCurveHandler

ROCPoint - Class in procope.evaluation.networkperformance

One single point in a ROC curve consisting of a true positive rate and a false positive rate value.

ROCPoint(float, float) - Constructor for class procope.evaluation.networkperformance.ROCPoint

Initialization constructr.